Mesenchymal Stem Cell - Derived Extracellular Vesicles Isolation and their Protein Cargo Characterisation -- Clinical Proteomics for the Analysis of Circulating Extracellular Vesicles -- Utilization of Laser Capture Microdissection Coupled to Mass Spectrometry to Uncover the Proteome of Cellular Protrusions -- Isolation of Apoplastic Fluid From Woody Plants Leaves: Grapevine and Coffee as a Case Study -- Shotgun Proteomics for L3 and L4 Anisakis simplex Development Stages -- A Primer and Guidelines for Shotgun Proteomic Analysis in Non-Model Organisms -- SWATH-MS Protocols in Human Diseases -- Serum Proteomic Profiling in Rheumatoid Arthritis by Antibody Suspension Bead Arrays -- Human Blood Plasma Investigation Employing 2d Uplc-Udmse Data-Independent Acquisition Proteomics -- Metaproteomics Analysis of Host-Microbiota Interfaces -- Mass Spectrometry-Based Analysis of Mycobacterial Single-Colony Proteome -- Proteogenomic Approach for Mycobacterium Tuberculosis Investigation -- Shotgun Proteomics for Food Microorganism Detection -- Shotgun Proteomics and Protein-Based Bioinformatics for the Characterization of Food-Derived Bioactive Peptides -- FTSC-labeling Coupled with 2DE-LC-MS/MS Analysis of Complex Protein Mixtures for Identification and Relative Quantification of Tissue Carbonylome -- Mass Spectrometry-Based Proteomics for Analysis of Hydrophilic Phosphopeptides -- Rapid Shotgun Phosphoproteomics Analysis -- System-wide Profiling Of Protein-Complexes Via Size Exclusion Chromatography-Mass Spectrometry (SEC-MS) -- Qualitative and Quantitative Shotgun Proteomics Data Analysis from Data-Dependent Acquisition Mass Spectrometry -- The jPOST Repository as a Public Data Repository for Shotgun Proteomics.

This edition details a collection of specific shotgun proteomics-based laboratory techniques and applications developed in leading laboratories and proteomics units worldwide. Chapters cover a broad range of topics covering, shotgun proteomics of extracellular vesicles and subcellular structures, shotgun proteomics in non-model organisms, clinical proteomics, food proteomics, analysis of post-translational modifications and protein complexes, and data processing and storage. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Shotgun Proteomics: Methods and Protocols aims to be an up-to-date guide for researchers seeking to understand the proteome of any given biological sample.